Codeprogrammers/codecraft-init-script — pull request #10 by Paswaru (2012-04-10 22:25:09+00:00)
Title: +# 0.2.0 - ADD: Support for multiple instances of minecraft server under different usernames.

I don't recommend adding this into the main branch. I could see people not getting the security setup properly, or possible just don't document it as a feature but leave the code in place for advance users.

Make two user accounts, one for each instance.
Create two separate directories, one for each instance.
Make a copy of the script for each instance in init.d (i.e. /init.d/minecraft, /init.d/devcraft).
Edit the individual copies of the scripts to match the settings for each instance.

Each user account shouldn't have access to the other. A separate privileged account should be responsible for copying changes between instances.